Bioreactors and some chemical reactors are often isolated from the environment for many reasons, including for maintaining sterility, to prevent contamination, or for operator or environmental safety. Obtaining samples from such reactors can be difficult because of these needs for isolation. However, often the conditions in the reactor cannot be properly controlled without measuring properties within the reactor. Although some methods exist for determining or estimating the conditions in the reactor, such conventional methods are generally not able to utilize the information obtained to alter and/or control the biologically and/or chemically active environments to improve the conditions and product yield of the systems. Accordingly, systems and methods that provide sampling and control of reactors or other systems would be desirable.